IF YOU CAN’T TRAVEL to the world’s celebrated architectural relics—places like the Roman coliseum, Petra, Ephesus or Pompeii—you could probably find some good substitutes closer to home. They may lack the grand scale of say, the Parthenon, or the derelict beauty of Venice, but lots of places on our young soil still evoke fantasy, mystery and loss in their unexplained neglect.

A few examples: Bannerman Castle built on a outcropping in the Hudson River near Beacon, Seaview Hospital on Staten Island, the Richmond Hill Republican Club in Queens, large swathes of Newark.

And, within a short subway ride: the Tobacco Warehouse and Empire Stores in between the Brooklyn and Manhattan bridges.

I was on a recent tour of the Empire Stores, a massive complex of former coffee warehouses. David Lowin from the Brooklyn Bridge Park Corp., told me there were still coffee beans scattered on the floor upstairs. I sniffed, but couldn’t smell them: The warehouses have been empty more than 50 years. Dating to 1869, they are among the last waterfront warehouses of their type here. Even for buildings of utility, they have elegant bearing: Romanesque Revival—a style frequently seen on civic buildings and college campuses—iron shutters and generous arched windows like so many eyes looking out onto the water. They’ve long captured people’s imagination: they were famously photographed by Berenice Abbott for the Federal Art Project of the WPA and remain a mysterious, hulking sight.

The state issued a request for proposals a few years ago, awarded one and took it back after the selected developer failed to build as promised. Since then, no one has stepped up to the enormous task of renovating this fantastic block—our own monument to Brooklyn’s commercial waterfront history. If you want to know how these could be re-imagined, trek out to Red Hook. The warehouses along the waterfront, also used for coffee storage from the same year, now contain small businesses and artist studios, and are anchored by a Fairway supermarket.

The Empire complex remains in limbo while the city, state and the feds resolve litigation involving this and the nearby Tobacco Warehouse. My story in The Wall Street Journal reports on the lawsuit, which recently ruled in favor of the plaintiffs who fought to reinstate the buildings in federally protected parkland after the state and city duped the National Park Service into de-parking them.

In the case of the Tobacco Warehouse, a striking urban relic, a proposal was granted to a local arts organization to build a theater in the space. It was a gnarly issue. The arts organization is well-regarded in the community—no contest there. But community members didn’t have much regard for the way the city and state took the land away and gave it to a private party without public hearing or solicitation of comment. It also didn’t sit well with the folks who discovered, through the Freedom of Information Act, that the state lied to the parks service about the Tobacco Warehouse’s usability. For six years, the public enjoyed the roofless ruins as picnic grounds, a performance space, and for, as the judge ruled in his findings, “building Frosty the Snowman.”

Photo: Natalie Keyssar

The Tobacco Warehouse could easily have been another derelict relic. But ongoing public use and enjoyment of it fostered a mindfulness of not only its majesty, but its history in much the same way such ruins are enjoyed in Europe, like the Carmo Convent in Lisbon, Abbaye de La Sauve-Majeure near Bordeaux and San Galgano in Tuscany. The Tobacco Warehouse is such a temple in its own way.

St. Ann’s Warehouse, the organization selected for the rehab, would have done a tasteful and mindful restoration. Its proposal had all the right stuff: community space, public access to the roofless courtyard, funding for the ongoing maintenance of the historic walls. Artistic director Susan Feldman told me she envisioned bringing a year-round cultural anchor to the park, and creating an arts hub like other great cultural waterfronts in the world—Avignon, London, Sidney.

“It was easy to combine our needs with the public’s needs,” she told me in a phone interview from London. St. Ann’s has been in a former spice warehouse the past 10 years (I swore I could still smell cardamom when I visited last week), and has to move by next year.

But in the end, the process by which the land became available—as murky as the waters of the East River—raised more suspicions than hopes for the site. The issues of unlawful privatization, secret back-door dealings and the notion that the very governmental agencies who are supposed to protect our lands could be pressured to give them up to developers, rightfully overrode the proposal.

“If they had gone through the process they should have, they would have had to go public and explore alternatives for St Ann’s,” said Peg Breen, the New York Landmarks Conservancy president, and a plaintiff in the suit. “You can’t ignore the breaking of all these federal laws, no matter how nice the group is.”

Until the ruling is final, it’s careful celebration of the almost-victory. The process has vexed all the parties involved. St. Ann’s is without a new home, the Brooklyn Bridge Park Corp. is without a much-needed and much-hoped for revenue stream and preservationists are justly leery of local government. The general public hasn’t spoken out yet, but the community groups who monitored the procedure—also plaintiffs in the lawsuit—have been vocal.

Joan Zimmerman, president of the Fulton Ferry Landing Association, which has fought a decades-long battle for a park here, said, “the simple reality and the great irony of this entire situation is that no park would have existed without the intercedence of the public.

“It was a meeting place for art and culture and education and that’s the way the community wants to preserve it.”